Algoritmy pro nalezení spojitých motivů na povrchu molekuly proteinu

Bc. Hana Šustrová

Master's thesis

Algorithms for searching of continuous motifs on surface of protein molecules

Abstract:

This diploma thesis is focused on searching of molecular surfaces using computational chemistry methods. Specifically, the thesis studies protein molecules, which have significant part in biochemistry of organisms. The aim of the thesis is finding amino acids, i. e. continual motifs, which are situated on the molecular surface. Before continual motifs searching, surface atoms are determined. Four approaches (NIN, SOV, Lattice and SAS) for searching of surface atoms are described in the thesis. Algorithms based on the approaches are implemented and tested on a group of proteins from Protein Data Bank. Further, an algorithm for recognizing surface continuous motifs (which utilizes results form previous approaches) is designed, implemented and tested on the above mentioned real proteins. Results of the tests are analyzed and the algorithms are compared with each other according to their accuracy and speed.

Keywords

van der Waals surface, Solvent Accessible Surface, SAS, contact/re-entrant surface, surface atoms, surface motifs, protein, Protein Data Bank, PDB, NIN algorithm, SOV algorithm, UCSF algorithm

Language used: Czech

Date on which the thesis was submitted / produced: 19. 5. 2006

Thesis defence

• Date of defence: 28. 6. 2006
• Supervisor: doc. RNDr. Radka Svobodová Vařeková, Ph.D.

Masaryk University

Faculty of Informatics

Master programme / field:
Applied Informatics / Applied Informatics